Residents in the town of Damboa said they were left completely defenceless after the security forces pulled out of the area following a militant attack two weeks ago.
In the latest violence, the extremists struck just before sundown yesterday, while locals prepared to break the Ramadan fast, and rampaged with no resistance until 5:00 am (0400 GMT), witnesses said.
"They killed many people. Women and children fled into the bush," said an official with the Damboa local government, who requested anonymity.
Boko Haram, a militant Islamist group in Nigeria blamed for slaughtering more than 2,000 civilians already this year, has increasingly targeted remote northeastern communities, razing entire villages while firing indiscriminately on the population.
"Most houses in the town have been burnt. Only a few still remain," said resident Ahmed Buba.
The militants and security forces clashed in Damboa earlier this month.
The military claimed it repelled the raid and even killed scores of insurgents, but locals told AFP that the security forces sustained heavy losses and pulled out of the area.
Those who escaped of the overnight raid fled to the state capital Maiduguri and sought shelter in the palace of the area's top cleric, Umar Garbai El-Kanemi, also known as the Shehu of Borno.
The survivors "lodged a complaint with the Shehu because there are no security forces in Damboa," the official said.
The military was not immediately available to comment on the attack in the deeply impoverished region, which often has limited mobile phone coverage.
Damboa resident Buba said the militants burnt the town's main market, as well as the home of the local government chairman and the area's top cleric.
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